Proteogenomics has revealed insights into the consequences of genomic aberrations and the altered biology of human breast (Mertins et al. PMID: 27251275), colo-rectal (Zhang et al PMID: 25043054), and ovarian (Zhang et al PMID: 27372738) cancers. The project of generating the data for the protein counterpart of human tumors from hundreds of individuals began in 2011 with the Clinical Proteomics Tumor Analysis Consortium of the National Institutes of Health. The technical challenges that accompanied this endeavor will be briefly highlighted. The efforts to achieve high reproducibility and repeatability for these high-density data sets will be presented. The current harmonized deep-scale proteomic and phosphoproteomic protocols will be discussed in the context of building batch-effect resistant analysis platforms for proteogenomics.
Dr. Townsend is a Professor in the Department of Medicine within the Divisions of Metabolism and Oncology at Washington University in St. Louis, MO. He directs the Proteomics Shared Resource to support the programs of the Siteman Comprehensive Cancer Center and the Institute of Clinical and Translational Sciences. His research interests include: i) discovery and validation of new cancer biology that could translate into new clinical paradigms and drug targets, protein biomarker of neurological disease, and identifying functional post-translational modifications. His most recent interest is using discovery and targeted proteomics to enlighten the biology of the understudied kinases as part of the “Illuminating the the Druggable Genome” initiative (https://commonfund.nih.gov/idg).